BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 2 7 5 27.50 0.24 2 2 15 13 21.10 0.43 3 2 16 14 21.10 0.43 4 2 17 15 26.79 0.39 5 2 52 50 21.12 0.42 6 2 53 51 21.09 0.43 7 2 108 106 21.27 0.35 8 2 109 107 21.09 0.43 9 3 6 3 37.05 0.64 10 3 7 4 29.35 0.07 11 3 17 14 27.48 0.24 12 3 107 104 27.84 0.14 13 3 108 105 22.85 0.43 14 4 7 3 37.18 0.58 15 4 8 4 110.50 23.56 16 4 17 13 28.38 0.12 17 4 106 102 30.26 1.07 18 4 107 103 29.55 0.79 19 6 52 46 127.89 4.12 20 7 17 10 180.72 4.30 21 8 18 10 249.24 5.43 22 8 19 11 154.24 2.40 23 8 42 34 128.11 4.11 24 12 52 40 128.04 4.13 25 13 46 33 128.06 4.14 26 13 47 34 128.05 4.14 27 14 46 32 127.98 4.12 28 14 47 33 127.98 4.12 29 14 49 35 128.03 4.13 30 14 52 38 128.04 4.13 31 15 45 30 128.01 4.12 32 15 46 31 127.95 4.12 33 15 47 32 127.97 4.12 34 15 48 33 127.95 4.12 35 15 52 37 127.98 4.12 36 15 109 94 127.98 4.12 37 15 110 95 127.95 4.12 38 15 111 96 121.98 1.34 39 16 44 28 127.98 4.12 40 16 45 29 127.98 4.12 41 16 52 36 127.98 4.13 42 16 109 93 103.27 1.47 43 17 42 25 128.11 4.12 44 17 43 26 128.09 4.12 45 17 106 89 127.96 4.12 46 17 107 90 128.02 4.13 47 17 108 91 127.98 4.12 48 17 109 92 127.81 4.05 49 18 42 24 128.12 4.12 50 18 43 25 128.09 4.11 51 18 45 27 128.09 4.12 52 18 46 28 128.09 4.12 53 19 42 23 128.12 4.12 54 19 43 24 128.16 4.10 55 20 40 20 128.27 4.10 56 20 41 21 128.19 4.11 57 20 42 22 128.13 4.12 58 20 43 23 128.17 4.10 59 21 38 17 128.38 4.10 60 21 39 18 128.34 4.11 61 21 40 19 128.28 4.11 62 22 27 5 142.69 1.55 63 22 28 6 142.69 1.55 64 22 38 16 128.40 4.09 65 22 39 17 128.37 4.10 66 22 41 19 128.28 4.10 67 23 26 3 150.44 0.75 68 23 27 4 142.69 1.55 69 23 28 5 142.69 1.54 70 23 37 14 128.44 4.08 71 23 38 15 128.42 4.08 72 24 28 4 142.69 1.54 73 24 29 5 142.69 1.55 74 24 30 6 138.44 0.39 75 24 33 9 128.66 4.04 76 24 36 12 128.48 4.08 77 24 37 13 128.46 4.08 78 24 38 14 128.44 4.08 79 24 39 15 128.45 4.08 80 24 104 80 128.45 4.08 81 25 29 4 142.69 1.55 82 25 30 5 138.75 0.35 83 25 31 6 135.21 1.02 84 30 33 3 163.27 0.93 85 30 101 71 141.96 0.96 86 32 90 58 165.46 1.57 87 32 91 59 199.30 4.01 88 33 36 3 260.00 4.57 89 33 88 55 147.51 0.74 90 33 89 56 147.84 0.58 91 33 90 57 148.40 0.85 92 34 37 3 179.81 1.28 93 34 89 55 147.37 0.68 94 34 90 56 147.52 0.74 95 34 91 57 156.66 1.99 96 35 88 53 137.50 0.17 97 35 89 54 141.57 1.73 98 36 87 51 135.36 0.89 99 36 88 52 135.26 0.93 100 39 86 47 128.57 4.07 101 44 78 34 128.12 4.11 102 44 79 35 128.14 4.11 103 44 80 36 128.20 4.08 104 45 78 33 128.12 4.12 105 46 78 32 128.09 4.12 106 48 76 28 128.12 4.11 107 48 77 29 128.09 4.12 108 48 78 30 127.99 4.12 109 49 52 3 224.56 3.45 110 50 60 10 128.80 4.03 111 50 63 13 128.51 4.09 112 50 64 14 128.50 4.09 113 51 60 9 128.75 4.06 114 52 111 59 129.12 4.07 115 53 110 57 129.11 4.07 116 53 111 58 128.99 4.08 117 54 59 5 144.59 2.24 118 54 60 6 135.11 0.83 119 54 111 57 128.96 4.08 120 55 59 4 165.75 2.06 121 55 110 55 128.97 4.09 122 55 111 56 128.95 4.08 123 55 112 57 128.79 4.04 124 56 59 3 183.25 0.90 125 56 60 4 172.38 1.26 126 57 60 3 186.19 0.58 127 57 61 4 172.47 1.21 128 58 61 3 197.47 3.10 129 58 62 4 173.81 2.68 130 59 62 3 195.61 2.18 131 59 63 4 174.47 2.36 132 59 76 17 127.51 4.09 133 59 111 52 128.72 4.04 134 59 112 53 128.44 4.08 135 60 63 3 194.47 4.09 136 60 64 4 181.80 1.30 137 61 64 3 199.30 3.59 138 61 65 4 182.43 1.62 139 62 65 3 189.56 1.95 140 62 66 4 182.43 1.61 141 62 74 12 128.17 4.12 142 62 76 14 127.91 4.11 143 63 66 3 195.59 3.50 144 63 67 4 182.37 1.65 145 63 76 13 128.08 4.11 146 64 67 3 199.07 5.55 147 64 68 4 182.37 1.65 148 65 68 3 206.45 1.86 149 65 69 4 174.66 0.04 150 65 72 7 144.12 1.53 151 65 74 9 128.22 4.11 152 66 69 3 188.25 1.98 153 66 70 4 159.65 1.42 154 66 74 8 128.22 4.11 155 66 75 9 128.16 4.11 156 66 76 10 128.16 4.11 157 67 70 3 204.94 3.21 158 69 72 3 219.96 2.23 159 70 73 3 216.92 1.60 160 76 111 35 127.97 4.12 161 76 112 36 127.93 4.12 162 77 110 33 128.09 4.12 163 77 111 34 127.93 4.12 164 77 112 35 126.62 3.75 165 78 109 31 128.06 4.11 166 78 110 32 127.98 4.12 167 79 109 30 128.10 4.11 168 79 110 31 128.00 4.12 169 79 112 33 127.98 4.12 170 80 106 26 128.07 4.17 171 80 108 28 128.19 4.08 172 80 109 29 128.10 4.12 173 80 110 30 128.12 4.11 174 81 108 27 128.20 4.08 175 81 109 28 128.19 4.08 176 81 110 29 128.15 4.11 177 82 106 24 128.32 4.12 178 82 107 25 128.28 4.10 179 82 108 26 128.24 4.09 180 83 103 20 128.24 4.04 181 83 105 22 128.35 4.11 182 83 106 23 128.32 4.12 183 83 107 24 128.31 4.12 184 84 103 19 128.45 4.08 185 84 104 20 128.40 4.11 186 84 105 21 128.36 4.11 187 84 107 23 128.35 4.11 188 85 100 15 128.59 4.07 189 85 101 16 128.56 4.08 190 85 102 17 128.50 4.08 191 85 103 18 128.50 4.08 192 86 100 14 128.65 4.04 193 86 101 15 128.59 4.07 194 86 104 18 128.50 4.08 195 86 105 19 128.50 4.08 196 87 98 11 135.38 0.86 197 87 99 12 134.34 1.22 198 87 100 13 128.65 4.04 199 88 98 10 140.68 1.77 200 88 99 11 135.26 0.92 201 88 101 13 134.71 1.12 202 89 96 7 149.40 0.07 203 89 97 8 146.02 0.27 204 89 98 9 142.96 0.62 205 90 96 6 155.10 2.78 206 90 97 7 149.15 0.18 207 90 99 9 147.60 0.54 208 91 95 4 220.37 5.62 209 91 96 5 156.66 2.00 210 92 95 3 261.92 1.26 211 92 97 5 180.45 4.41